Trichoderma & P. vulgaris interaction

Things to do

Things done

Loogbook

Many beans are contaminated with fungi. :( sadly we need to wait for a new opportunity and new set to measuer VOCs.

This is a 3rd set of beans. This work was mady by Emmy.

Intergenic sequences in T.atroviride

Things to do

Analyze 20 matches.

Correct mistakes in coordinates in 0bp file. Run Blast to overview check.

Prediction again by Augustus.

Run analysis again with FilteringBLASTsFromAugustusPredictions.R in /Scripts & Data.

Things done

Analyzed.

Corrected.

Prediction done.

Re-analyzing.

Loogbook

Just 20 hits. Seems there is something wrong. I see the coordinates in 0bp file and they are wrong!!! in file GettingSequences.R (I cant find the Script were I extract 0,480,1020,770), but this one works. And I create the file IntergenicFastaCorrected.fas (extracts just 0bp seqs).

Corrected.

Prediction

Submitting JGI

Wed Oct 03 00:31:47 CEST 2012 - Message:

Details of your job:

Prediction job ID: predqHPrnxqC

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Resutls JGI

Wed Oct 03 00:31:47 CEST 2012 - Message:

Details of your job:

Prediction job ID: predqHPrnxqC

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Your AUGUSTUS prediction job predqH**** finished.

Submitting 454

Wed Oct 03 00:42:29 CEST 2012 - Message:

Details of your job:

Prediction job ID: prediLs9Y6C3

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes

Ignore conflictes with other strand: false

Results 454

Wed Oct 03 00:42:29 CEST 2012 - Message:

Details of your job:

Prediction job ID: prediLs9Y6C3

Parameter archive: parameters.tar.gz

Genome file: IntergenicFastaCorrected.fas

User set UTR prediction: false

Report genes on: both strands

Alternative transcripts: none

Allowed gene structure: predict any number of (possibly partial) genes